Article
Biochemistry & Molecular Biology
Frederic B. Bastian, Julien Roux, Anne Niknejad, Aurelie Comte, Sara S. Fonseca Costa, Tarcisio Mendes de Farias, Sebastien Moretti, Gilles Parmentier, Valentine Rech de Laval, Marta Rosikiewicz, Julien Wollbrett, Amina Echchiki, Angelique Escoriza, Walid H. Gharib, Mar Gonzales-Porta, Yohan Jarosz, Balazs Laurenczy, Philippe Moret, Emilie Person, Patrick Roelli, Komal Sanjeev, Mathieu Seppey, Marc Robinson-Rechavi
Summary: Bgee is a database that allows retrieval and comparison of gene expression patterns in multiple animal species using curated healthy wild-type data, enabling the detection of expression conditions for any single gene across different species. It integrates various data types and ensures consistent data annotation and processing for cross-species comparisons.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Plant Sciences
Biswajit Karan, Satyajit Mahapatra, Sitanshu Sekhar Sahu, Dev Mani Pandey, Sumit Chakravarty
Summary: In this study, four genomic information-based models were used to predict the interaction between rice and blast fungus. The predicted interactions achieved high accuracy, which was confirmed through machine learning evaluation. These predicted interactions are valuable for drug design in the field of plant science.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Multidisciplinary Sciences
Bao-Lin Zhang, Wu Chen, Zefu Wang, Wei Pang, Meng -Ting Luo, Sheng Wang, Yong Shao, Wen-Qiang He, Yuan Deng, Long Zhou, Jiawei Chen, Min -Min Yang, Yajiang Wu, Lu Wang, Hugo Fernandez-Bellon, Sandra Molloy, Helene Meunler, Fanelie Wanert, Lukas Kuderna, Tomas Marques-Bonet, Christian Roos, Xiao-Guang Qi, Ming Li, Zhiji Liu, Mikkel Heide Schierup, David N. Cooper, Jianquan Liu, Yong-Tang Zheng, Guojie Zhang, Dong-Dong Wu
Summary: Through phylogenomic analysis of 12 macaque species, we discovered that the fascicularis group originated from an ancient hybridization event between the sinica and silenus groups around 3.45 to 3.56 million years ago. The X chromosomes and low-recombination regions showed equal contributions from each parental lineage, suggesting their importance in maintaining hybrid integrity. We also identified reproduction-associated genes and confirmed susceptibility to HIV-1 infection in all extant Western silenus species. Our study provides new insights into macaque evolution and highlights a rare hybrid speciation event in primates.
Article
Biology
Baihui Wu, Hanzhi Zhang, Menghan Zhang
Summary: The origin of tone, or tonogenesis, is a fascinating aspect of language evolution and human cognition. Various hypotheses have been proposed to explain the origin of tones in tonal languages, but they have not been quantitatively tested. In this study, we analyzed 106 Sino-Tibetan languages, of which around 70% are tonal, to investigate the likelihood of different tonogenetic mechanisms. Our results showed a strong phylogenetic pattern in the presence of tones, suggesting that Proto-Sino-Tibetan languages were most likely non-tonal. We also found that tonal origin was associated with specific phonological changes, such as the loss of syllable-final consonants and changes in vowel quality.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Paul D. Thomas, Dustin Ebert, Anushya Muruganujan, Tremayne Mushayahama, Laurent-Philippe Albou, Huaiyu Mi
Summary: PANTHER is a user-focused knowledgebase that stores results of extensive phylogenetic reconstruction pipelines and provides manual review and annotation of function evolution events, aiding in protein sequence analysis tasks.
Article
Multidisciplinary Sciences
Blake V. Dickson, Jennifer A. Clack, Timothy R. Smithson, Stephanie E. Pierce
Summary: The analysis of humeri shows that changes in shape are driven by both ecology and phylogeny, with functional trade-offs related to locomotor performance. The evolution of terrestrial locomotion in tetrapods involved the acquisition of limb-based locomotion, leading to the diversification of terrestrial tetrapods and establishment of modern ecological niches. Stem tetrapods may have used transitional gaits during the initial stages of land exploration, stabilized by opposing selective pressures of amphibious habits.
Article
Genetics & Heredity
Thomas Hollin, Lukasz Jaroszewski, Jason E. Stajich, Adam Godzik, Karine G. Le Roch
Summary: The RNA binding domain abundant in apicomplexans (RAP) is widely present in various organisms with a conserved structure for specific RNA binding. The N-terminal and C-terminal regions of RAP proteins have different functions, with the highly conserved RAP domain in the C-terminal possibly playing a crucial role in ensuring protein function.
MICROBIAL GENOMICS
(2021)
Review
Plant Sciences
David C. Baulcombe
Summary: My research career began with an interest in plant gene regulation and experimentation with various systems. Eventually, I focused on plant viruses and explored topics beyond virology, including RNA silencing, epigenetics, and genome evolution. I have learned about research approaches, finding tractable systems, and applying academic research in real-world contexts. My current projects address the definition of epigenetics, the arms race concept of disease resistance, and Darwin's abominable mystery.
ANNUAL REVIEW OF PLANT BIOLOGY
(2023)
Review
Plant Sciences
Yuanpeng Fang, Junmei Jiang, Xiaolong Hou, Jiyuan Guo, Xiangyang Li, Degang Zhao, Xin Xie
Summary: The evolution of gene families is crucial for understanding the evolutionary history and biodiversity of plants, as well as explaining their tolerance to environmental stresses. Studying the molecular evolution of plant gene families helps to gain insights into these important processes.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Birgit H. M. Meldal, Carles Pons, Livia Perfetto, Noemi Del-Toro, Edith Wong, Patrick Aloy, Henning Hermjakob, Sandra Orchard, Pablo Porras
Summary: The EMBL-EBI Complex Portal is a knowledgebase of macromolecular complexes that provides persistent stable identifiers, with data freely available and downloadable. In collaboration with other databases, the yeast complexome was curated, leading to an increase in curated complexes compared to the previous dataset. The analysis showed that genes in complexes have more genetic interactions, are more multifunctional, and are often involved in nucleic acid-related metabolic processes.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Evgeny S. Gerasimov, Anna A. Gasparyan, Dmitry A. Afonin, Sara L. Zimmer, Natalya Kraeva, Julius Lukes, Vyacheslav Yurchenko, Alexander Kolesnikov
Summary: Uridine insertion/deletion (U-indel) editing of mitochondrial mRNA, unique to the protistan class Kinetoplastea, generates canonical as well as potentially non-productive editing events. Analysis reveals that a multitude of editing events are guided by a limited set of gRNAs, with each gRNA possessing the inherent ability to guide both canonical and non-canonical editing.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Plant Sciences
Xin-Xing Fu, Jian Zhang, Guo-Qiang Zhang, Zhong-Jian Liu, Zhi-Duan Chen
Summary: Plant sigma factors are key regulators of chloroplast gene expression and differentiation, with evolutionary history showing acquisition from cyanobacteria through endosymbiotic gene transfers. The expansion of sigma factors in plants, especially flowering plants, is driven by gene duplications, contributing to their functional diversification.
JOURNAL OF SYSTEMATICS AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Shilin Tian, Jiaming Zeng, Hengwu Jiao, Dejing Zhang, Libiao Zhang, Cao-qi Lei, Stephen J. Rossiter, Huabin Zhao
Summary: Bats, especially fruit bats, have unique immunological adaptations that may explain their role as natural hosts of zoonotic viruses. Comparative analysis of 12 bat species, including six fruit bats, reveals that the evolutionary rates of immunity-related genes are higher in fruit bats. These bats share lineage-specific genetic changes in immune-related genes, resulting in dampened inflammatory responses. These findings shed light on why fruit bats are frequently identified as viral hosts.
Article
Veterinary Sciences
Claudia Techera, Ana Marandino, Gonzalo Tomas, Sofia Grecco, Martin Hernandez, Diego Hernandez, Yanina Panzera, Ruben Perez
Summary: Chicken anaemia virus (CAV) is a prevalent pathogen causing immunosuppression in chickens, with a highly variable genome. Through analyzing CAV strains from Uruguay and conducting global comparative analysis, it was found that the virus emerged in the early 1900s, underwent global spreading, and spread through multiple migratory events in South America.
Review
Cell Biology
Bowen Liu, Jinling Cao, Xiangyun Wang, Chunlei Guo, Yunxia Liu, Tianjiao Wang
Summary: This paper reviews the biogenesis, classification, subcellular localization, and action mechanism of tsRNAs, as well as the association between chemical modifications of tRNAs and the production and functions of tsRNAs. It further summarizes the molecular mechanisms of tsRNAs in diseases such as immunity, metabolism, and malignancy, and evaluates the potential of tsRNAs as biomarkers and therapeutic targets. Additionally, it introduces several resource databases for analyzing tsRNAs, and discusses the challenges and future directions in this field.
CELL DEATH & DISEASE
(2022)
Article
Genetics & Heredity
Kyung Mo Kim, Hanna Choe, Byung Kwon Kim, Arshan Nasir
Article
Microbiology
Arshan Nasir, Kyung Mo Kim, Gustavo Caetano-Anolles
FRONTIERS IN MICROBIOLOGY
(2017)
Article
Microbiology
Shahana S. Malik, Syeda Azem-e-Zahra, Kyung Mo Kim, Gustavo Caetano-Anolles, Arshan Nasir
FRONTIERS IN MICROBIOLOGY
(2017)
Letter
Biochemistry & Molecular Biology
Kelsey Caetano-Anolles, Derek Caetano-Anolles, Arshan Nasir, Kyung Mo Kim, Gustavo Caetano-Anolles
Article
Microbiology
Ji-Sun Kim, Hanna Choe, Kyung Mo Kim, Yu-Ri Lee, Moon-Soo Rhee, Doo-Sang Park
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2018)
Article
Multidisciplinary Sciences
Gahyung Lee, Sang-Heon Lee, Kyung Mo Kim, Choong-Min Ryu
SCIENTIFIC REPORTS
(2017)
Article
Microbiology
Ji-Sun Kim, Hanna Choe, Yu-Ri Lee, Kyung Mo Kim, Doo-Sang Park
JOURNAL OF MICROBIOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Derek Caetano-Anolles, Arshan Nasir, Kyung Mo Kim, Gustavo Caetano-Anolles
JOURNAL OF MOLECULAR EVOLUTION
(2019)
Article
Multidisciplinary Sciences
Hyeonsoo Jeong, Bushra Arif, Gustavo Caetano-Anolles, Kyung Mo Kim, Arshan Nasir
SCIENTIFIC REPORTS
(2019)
Article
Evolutionary Biology
Rijja Hussain Bokhari, Nooreen Amirjan, Hyeonsoo Jeong, Kyung Mo Kim, Gustavo Caetano-Anolles, Arshan Nasir
GENOME BIOLOGY AND EVOLUTION
(2020)
Article
Multidisciplinary Sciences
Yong-Soon Park, Seon-Kyu Kim, Seon-Young Kim, Kyung Mo Kim, Choong-Min Ryu
Article
Genetics & Heredity
Kyuin Hwang, Hanna Choe, Arshan Nasir, Kyung Mo Kim
Summary: Polaromonas vacuolata KCTC 22033(T) is a unique bacterium isolated from beneath the Antarctic sea ice, showing genomic features related to adaptation to salinity, cold, and starvation, as well as genes likely acquired from species outside its genus.
Article
Genetics & Heredity
Kyuin Hwang, Hanna Choe, Kyung Mo Kim
Summary: Nocardioides aquaticus is a versatile bacterium isolated from Ekho Lake in Antarctica, capable of thriving in wide ranges of temperature and salinity. Its genome contains genes advantageous to oligotrophic bacteria and genes associated with high tolerance to strong environmental gradients.
Article
Evolutionary Biology
Gustavo Caetano-Anolles, Arshan Nasir, Kyung Mo Kim, Derek Caetano-Anolles
EVOLUTIONARY BIOINFORMATICS
(2018)
Article
Biochemistry & Molecular Biology
Arshan Nasir, Kyung Mo Kim, Gustavo Caetano-Anolles